Complex: MBP-BORF2 (large subunit of EBV ribonucleotide reductase with n-terminal MBP tag)
Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Ribonucleoside-diphosphate reductase large subunit
Complex: APOBEC3Bctd-mychis (human APOBEC3B protein with c-terminal mychis tag)
Protein or peptide: DNA dC->dU-editing enzyme APOBEC-3B
Ligand: ZINC ION
Function / homology
Function and homology information
mRNA Editing: C to U Conversion / Formation of the Editosome / release from viral latency / single-stranded DNA cytosine deaminase / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate ...mRNA Editing: C to U Conversion / Formation of the Editosome / release from viral latency / single-stranded DNA cytosine deaminase / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / retrotransposon silencing / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / P-body / outer membrane-bounded periplasmic space / defense response to virus / DNA replication / periplasmic space / innate immune response / DNA damage response / RNA binding / zinc ion binding / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm Similarity search - Function
Ribonucleotide reductase large subunit, Alphaherpesviruses / Novel AID APOBEC clade 2 / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain / APOBEC/CMP deaminase, zinc-binding ...Ribonucleotide reductase large subunit, Alphaherpesviruses / Novel AID APOBEC clade 2 / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein Similarity search - Domain/homology
Ribonucleoside-diphosphate reductase large subunit / Maltose/maltodextrin-binding periplasmic protein / DNA dC->dU-editing enzyme APOBEC-3B Similarity search - Component
Biological species
Epstein-Barr virus (Epstein-Barr virus) / Homo sapiens (human) / Human gammaherpesvirus 4 (Epstein-Barr virus)
Method
single particle reconstruction / cryo EM / Resolution: 2.55 Å
National Institutes of Health/National Cancer Institute (NIH/NCI)
United States
Citation
Journal: Sci Adv / Year: 2022 Title: Cryo-EM structure of the EBV ribonucleotide reductase BORF2 and mechanism of APOBEC3B inhibition. Authors: Nadine M Shaban / Rui Yan / Ke Shi / Sofia N Moraes / Adam Z Cheng / Michael A Carpenter / Jason S McLellan / Zhiheng Yu / Reuben S Harris / Abstract: Viruses use a plethora of mechanisms to evade immune responses. A recent example is neutralization of the nuclear DNA cytosine deaminase APOBEC3B by the Epstein-Barr virus (EBV) ribonucleotide ...Viruses use a plethora of mechanisms to evade immune responses. A recent example is neutralization of the nuclear DNA cytosine deaminase APOBEC3B by the Epstein-Barr virus (EBV) ribonucleotide reductase subunit BORF2. Cryo-EM studies of APOBEC3B-BORF2 complexes reveal a large >1000-Å binding surface composed of multiple structural elements from each protein, which effectively blocks the APOBEC3B active site from accessing single-stranded DNA substrates. Evolutionary optimization is suggested by unique insertions in BORF2 absent from other ribonucleotide reductases and preferential binding to APOBEC3B relative to the highly related APOBEC3A and APOBEC3G enzymes. A molecular understanding of this pathogen-host interaction has potential to inform the development of drugs that block the interaction and liberate the natural antiviral activity of APOBEC3B. In addition, given a role for APOBEC3B in cancer mutagenesis, it may also be possible for information from the interaction to be used to develop DNA deaminase inhibitors.
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